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Implement automated linting via GitHub Actions and Pre-Commit #293

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merged 91 commits into from
Dec 21, 2023

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kedhammar
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This is a big PR containing both the implementation of automated linting as well a fixes across the entire repo to ensure we kick things off from a place of passing all checks.

The fixes are largely non-invasive and superficial, so hopefully a thorough review and some rudimentary testing will be sufficient to accept the PR, but I'm not sure yet.

The commit history is very messy as I've been doing a lot of testing 😆

@kedhammar
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During sporadic testing of this PR w. Python 3.10 on Stage, it was apparent some Pandas code become outdated and had to be updated.

@kedhammar
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Suggested review (simplified)

New files

  • .github/workflows/lint-code.yml
  • .pre-commit-config.yaml
  • .git-blame-ignore-revs
  • requirements-dev.txt
  • pyproject.toml
  • README.md
  • conda_env.yml

Manually changed files

  • .gitignore
  • requirements.txt
  • setup.py

Manual commits

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@alneberg alneberg left a comment

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Very nice work!

@kedhammar kedhammar merged commit 802be85 into NationalGenomicsInfrastructure:master Dec 21, 2023
kedhammar added a commit that referenced this pull request Jan 4, 2024
Fix issues appearing after deploment of PR #293
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3 participants